[{"_1":2,"_206":-5,"_207":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_179":180},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_95":96,"_120":121,"_168":-5,"_169":11,"_170":21,"_171":11,"_172":-5,"_173":11,"_174":-5,"_175":176,"_177":122,"_178":-7},"canonicalUrl","https://hub.docker.com/r/staphb/salmid/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","staphb","reponame","salmid","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_50":51,"_53":54,"_55":56,"_57":11,"_58":59,"_60":61,"_62":63,"_43":35,"_32":33,"_65":66,"_67":52,"_68":69,"_70":71,"_72":73,"_74":-5,"_75":69,"_76":77,"_78":11,"_79":33,"_80":81,"_86":11,"_87":88,"_92":33,"_93":94},"categories",[42,47],{"_43":44,"_45":46},"name","Machine learning & AI","slug","machine-learning-and-ai",{"_43":48,"_45":49},"Data science","data-science","content_types",[52],"image","date_registered","2019-04-12T19:32:25.290328Z","description","Rapid confirmation of Salmonella spp. and subspp. from sequence data","is_private","last_updated","2019-04-30T13:56:10.09245Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[64],"application/vnd.docker.container.image.v1+json","pull_count",20725,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# [docker-builds](#)\nThis repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of programs used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.\n\nEach Dockerfile lists author/maintainer for that specific Docker image, but the authors/maintainers of the docker images are:\n * [@kapsakcj](https://github.com/kapsakcj)\n * [@k-florek](https://github.com/k-florek)\n * [@garfinjm](https://github.com/garfinjm)\n * [@kevinlibuit](https://github.com/kevinlibuit)\n * [@Ikkik](https://github.com/Ikkik)\n\nIf you would like to contribute with your own Docker image or perhaps improve upon the existing images, please fork the repository, make your changes/additions, and submit a pull request. If you are having an issue with an existing image, please submit an issue. We welcome any and all feedback! \n[See more details on how to contribute here](https://staph-b.github.io/docker-builds/contribute/)\n\n## [Docker User Guide](https://staph-b.github.io/docker-builds/)\nWe have also created a user guide that outlines methods and best practices for using and developing docker containers. \n[Docker User Guide](https://staph-b.github.io/docker-builds/)\n\n## [Available Docker images](https://hub.docker.com/r/staphb/)\n| Software | Version | Link |\n| :--------: | :-------: | -------- |\n| [seqyclean](https://hub.docker.com/r/staphb/seqyclean)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqyclean.svg?style=popout)](https://hub.docker.com/r/staphb/seqyclean) | 1.10.09 | https://github.com/ibest/seqyclean |\n| [SalmID](https://hub.docker.com/r/staphb/salmid)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/salmid.svg?style=popout)](https://hub.docker.com/r/staphb/salmid) | 0.1.23 | https://github.com/hcdenbakker/SalmID |\n| [mlst](https://hub.docker.com/r/staphb/mlst)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mlst.svg?style=popout)](https://hub.docker.com/r/staphb/mlst) | 2.16.2 | https://github.com/tseemann/mlst |\n| [SKESA](https://hub.docker.com/r/staphb/skesa)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/skesa.svg?style=popout)](https://hub.docker.com/r/staphb/skesa) | 2.3.0 | https://github.com/ncbi/SKESA |\n| [FastANI](https://hub.docker.com/r/staphb/fastani)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/fastani.svg?style=popout)](https://hub.docker.com/r/staphb/fastani) | 1.1 | https://github.com/ParBLiSS/FastANI |\n| [SRA-toolkit](https://hub.docker.com/r/staphb/sratoolkit/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sratoolkit.svg?style=popout)](https://hub.docker.com/r/staphb/sratoolkit) | 2.9.2 | https://github.com/ncbi/sra-tools |\n| [Lyve-SET (includes CG-Pipeline scripts and raxml)](https://hub.docker.com/r/staphb/lyveset/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/lyveset.svg?style=popout)](https://hub.docker.com/r/staphb/lyveset) | 1.1.4f, 2.0.1 (lyve-SET) | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |\n| [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/kraken.svg?style=popout)](https://hub.docker.com/r/staphb/kraken) | 1.0 | https://github.com/DerrickWood/kraken |\n| [SPAdes](https://hub.docker.com/r/staphb/spades/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/spades.svg?style=popout)](https://hub.docker.com/r/staphb/spades) | 3.12.0, 3.13.0 | http://cab.spbu.ru/software/spades/ |\n| [QUAST](https://hub.docker.com/r/staphb/quast/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/quast.svg?style=popout)](https://hub.docker.com/r/staphb/quast) | 5.0.0 | https://github.com/ablab/quast |\n| [Mash](https://hub.docker.com/r/staphb/mash/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/mash.svg?style=popout)](https://hub.docker.com/r/staphb/mash) | 2.1 | https://github.com/marbl/Mash |\n| [SerotypeFinder](https://hub.docker.com/r/staphb/serotypefinder/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/serotypefinder.svg?style=popout)](https://hub.docker.com/r/staphb/serotypefinder) | 1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image) | https://bitbucket.org/genomicepidemiology/serotypefinder/ |\n| [SeqSero](https://hub.docker.com/r/staphb/seqsero/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero.svg?style=popout)](https://hub.docker.com/r/staphb/seqsero) | 1.0.1 | https://github.com/denglab/SeqSero |\n| [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/seqsero2.svg?style=popout)](https://hub.docker.com/r/staphb/seqsero2) | 0.1.0 | https://github.com/denglab/SeqSero2/ |\n| [SISTR](https://hub.docker.com/r/staphb/sistr/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/sistr.svg?style=popout)](https://hub.docker.com/r/staphb/sistr) | 1.0.2 | https://github.com/peterk87/sistr_cmd |\n| [ABRicate](https://hub.docker.com/r/staphb/abricate/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/abricate.svg?style=popout)](https://hub.docker.com/r/staphb/abricate) | 0.8.7 | https://github.com/tseemann/abricate |\n| [Prokka](https://hub.docker.com/r/staphb/prokka/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/prokka.svg?style=popout)](https://hub.docker.com/r/staphb/prokka) | 1.13 | https://github.com/tseemann/prokka |\n| [Trimmomatic](https://hub.docker.com/r/staphb/trimmomatic/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/trimmomatic.svg?style=popout)](https://hub.docker.com/r/staphb/trimmomatic) | 0.38 | http://www.usadellab.org/cms/?page=trimmomatic |\n| [iqtree](https://hub.docker.com/r/staphb/iqtree/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/iqtree.svg?style=popout)](https://hub.docker.com/r/staphb/iqtree) | 1.6.7 | http://www.iqtree.org/ |\n| [Unicycler](https://hub.docker.com/r/staphb/unicycler/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/unicycler.svg?style=popout)](https://hub.docker.com/r/staphb/unicycler) | 0.4.7 | https://github.com/rrwick/Unicycler |\n| [Canu-Racon](https://hub.docker.com/r/staphb/canu-racon/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/canu-racon.svg?style=popout)](https://hub.docker.com/r/staphb/canu-racon) | 1.7.1 (Canu) 1.3.1 (Racon) 2.13 (minimap2) | https://canu.readthedocs.io/en/latest/ https://github.com/isovic/racon https://lh3.github.io/minimap2/ |\n|[Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/roary.svg?style=popout)](https://hub.docker.com/r/staphb/roary) | 3.12.0 | https://github.com/sanger-pathogens/Roary |\n|[CDC-SPN](https://hub.docker.com/r/staphb/cdc-spn/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cdc-spn.svg?style=popout)](https://hub.docker.com/r/staphb/cdc-spn) | 0.1 (no version) | https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |\n| [Shovill](https://hub.docker.com/r/staphb/shovill/)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/shovill.svg?style=popout)](https://hub.docker.com/r/staphb/shovill) | 1.0.4 | https://github.com/tseemann/shovill |\n| [BWA](https://hub.docker.com/r/staphb/bwa)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/bwa.svg?style=popout)](https://hub.docker.com/r/staphb/bwa) | 0.7.17 | https://github.com/lh3/bwa |\n| [Samtools](https://hub.docker.com/r/staphb/samtools)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/samtools.svg?style=popout)](https://hub.docker.com/r/staphb/samtools) | 1.9 | https://github.com/samtools/samtools |\n| [cfsan-snp-pipeline](https://hub.docker.com/r/staphb/cfsan-snp-pipeline)
[![docker pulls](https://img.shields.io/docker/pulls/staphb/cfsan-snp-pipeline.svg?style=popout)](https://hub.docker.com/r/staphb/cfsan-snp-pipeline) | 2.0.2 | https://github.com/CFSAN-Biostatistics/snp-pipeline |\n\nYou can also view the list of images on Docker hub here: https://hub.docker.com/r/staphb/\n","has_starred","hub_user","immutable_tags_settings",{"_82":11,"_83":84},"enabled","rules",[85],".*","is_automated","permissions",{"_89":21,"_90":11,"_91":11},"read","write","admin","user","storage_size",675467290,"orgData",{"_97":98,"_99":100,"_101":102,"_103":33,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":115,"_116":107,"_117":118,"_119":21},"id","2879f6c1219644f08dac94f6ffde26a2","uuid","2879f6c1-2196-44f0-8dac-94f6ffde26a2","type","organization","orgname","full_name","StaPH-B","location","","company","State Public Health Bioinformatics Community","profile_url","https://staphb.org","date_joined","2018-06-07T13:55:18.804584Z","gravatar_url","https://www.gravatar.com/avatar/771cd3ec8b1da0c8121aeda371c8bde4?s=80&r=g&d=mm","gravatar_email","badge","open_source","is_active","recentTags",[122,158],{"_123":52,"_124":125,"_126":127,"_97":128,"_129":130,"_58":147,"_148":125,"_149":33,"_150":64,"_43":151,"_152":153,"_154":138,"_155":147,"_156":73,"_157":21},"content_type","creator",3229322,"full_size",239831001,52646917,"images",[131],{"_132":133,"_134":135,"_136":107,"_137":138,"_139":140,"_141":142,"_143":107,"_144":-5,"_145":127,"_70":73,"_146":-5},"architecture","amd64","digest","sha256:8ba62c385e5d8785f9de28e6316b163f980a4e496de1a217b7bf6bf2aa7f501e","features","last_pulled","2026-10-08T05:22:32.726674793Z","last_pushed","2019-04-30T13:56:10Z","os","linux","os_features","os_version","size","variant","2019-04-30T13:56:09.688711Z","last_updater","last_updater_username","media_type","latest","repository",6971440,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_123":52,"_124":125,"_126":159,"_97":160,"_129":161,"_58":166,"_148":125,"_149":33,"_150":64,"_43":167,"_152":153,"_154":164,"_155":166,"_156":73,"_157":21},239587435,52646236,[162],{"_132":133,"_134":163,"_136":107,"_137":164,"_139":165,"_141":142,"_143":107,"_144":-5,"_145":159,"_70":73,"_146":-5},"sha256:849d43ab8fdfc266dd87eff8727b6075ad10a9e6893f2be360f1ff94fdd8e4b4","2026-10-06T23:11:16.234625172Z","2019-04-12T19:50:35Z","2019-04-12T19:50:34.900738Z","0.1.23","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":181,"_190":191,"_175":204,"_205":11},{"_40":182,"_50":185,"_53":54,"_55":56,"_57":11,"_58":59,"_60":61,"_62":186,"_43":35,"_32":33,"_65":66,"_67":52,"_68":69,"_70":71,"_72":73,"_74":-5,"_75":69,"_76":77,"_78":11,"_79":33,"_80":187,"_86":11,"_87":189,"_92":33,"_93":94},[183,184],{"_43":44,"_45":46},{"_43":48,"_45":49},[52],[64],{"_82":11,"_83":188},[85],{"_89":21,"_90":11,"_91":11},"tags",{"_192":193,"_194":-5,"_195":-5,"_196":197},"count",2,"next","previous","results",[198,201],{"_123":52,"_124":125,"_126":127,"_97":128,"_129":199,"_58":147,"_148":125,"_149":33,"_150":64,"_43":151,"_152":153,"_154":138,"_155":147,"_156":73,"_157":21},[200],{"_132":133,"_134":135,"_136":107,"_137":138,"_139":140,"_141":142,"_143":107,"_144":-5,"_145":127,"_70":73,"_146":-5},{"_123":52,"_124":125,"_126":159,"_97":160,"_129":202,"_58":166,"_148":125,"_149":33,"_150":64,"_43":167,"_152":153,"_154":164,"_155":166,"_156":73,"_157":21},[203],{"_132":133,"_134":163,"_136":107,"_137":164,"_139":165,"_141":142,"_143":107,"_144":-5,"_145":159,"_70":73,"_146":-5},[],"canDeleteTags","actionData","errors"]

staphb/salmid

Tags for staphb/salmid